This study attempts to determine the scale-dependent hierarchical spatial variation and longitudinal distributions of Sicyopterus japonicus year round. The distribution of S. japonicus in the Datuan Stream in northern Taiwan was surveyed during the fall and winter 2007, as well as the spring and summer of 2008. The spatial structure of S. japonicus density was modeled using geostatistics. The longitudinal distributions of S. japonicus density were then estimated using kriging and hydrology distance with nested variogram models. Variography results indicate that nested variogram models could reflect the hierarchical structure in the spatial variation of seasonal S. japonicus density, with the small, median, and large ranges representing three nested scales. Models for the four seasons were consistent in that they shared the same shape of variogram models with various ranges and sill values. This model shape consistency implies stationary spatial correlations in the longitudinal fish distribution across the four seasons. The Kriging geostatistical method based on the multiple scales nested variogram models also provided robust estimates of S. japonicus densities at unsampled sections. We conclude that S. japonicus densities exhibit hierarchical patterns and variation in the four seasons along the study stream. Geostatistical methods with a nested variograms and hydrological distance are a highly effective means of delineating the hierarchical structure in longitudinal patterns of S. japonicus density in each season, providing estimates of the S. japonicus density for hierarchically structured spatial distributions and expanding knowledge of S. japonicus beyond the limits imposed by spatial and temporal scales.